You should be able to get the Adventurer back: go to the top of the stairs (north twice from the main room of the library) and he should hear you from there. Then you can take the red sphere from him and use it to see into the clean room.
Though also, please do tell me what you were trying that wasn’t working! If reasonable commands were failing, I still consider that a bug.
And I’m very glad you’re enjoying it! I first got into IF through Colossal Cave and the early Infocom works, so I’ve always had a soft spot for modern puzzlefests. I’m glad it appeals to others too!